Really depends on which games you are talking about and what hardware you use, and what software settings you use.
Some games emulate better than others...
If you use an arcade monitor with an AVGA card and use the correct resolution, the games will look even closer to the real thing than with a PC monitor...
Vector games of course will look different... though color vectors emulate/look closer to the real thing than black and white vectors (specifically Asteroids and AD)
As for more modern NEOs and Fighters, I don't know... I never played those very much...